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tasks/Haplotyper.wdl
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| set -e | set -e | ||||
| export SENTIEON_LICENSE=192.168.0.55:8990 | export SENTIEON_LICENSE=192.168.0.55:8990 | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| if [ ${regions} ]; then | if [ ${regions} ]; then | ||||
| INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" | INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" | ||||
| else | else | ||||
| fi | fi | ||||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \ | ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \ | ||||
| -i ${recaled_bam} ${INTERVAL} \ | |||||
| -i ${recaled_bam} $INTERVAL \ | |||||
| --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf | --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf | ||||
| >>> | >>> | ||||
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